annotate QualityControl.xml @ 2:2f08fa7ab72c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [Quality Control]-->
<tool id="QualityControl" name="QualityControl" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.</description>
  <macros>
    <token name="@EXECUTABLE@">QualityControl</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in_cm &&
ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
#if $in_raw:
  mkdir in_raw &&
  ${ ' '.join(["ln -s '%s' 'in_raw/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _]) }
#end if
#if $in_postFDR:
  mkdir in_postFDR &&
  ${ ' '.join(["ln -s '%s' 'in_postFDR/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _]) }
#end if
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out &&
#end if
#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_cm &&
#end if
#if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_feat &&
#end if
#if $in_contaminants:
  mkdir in_contaminants &&
  ln -s '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
#end if
#if $in_trafo:
  mkdir in_trafo &&
  ${ ' '.join(["ln -s '%s' 'in_trafo/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _]) }
#end if

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in_cm
'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
#if $in_raw:
  -in_raw
  ${' '.join(["'in_raw/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _])}
#end if
#if $in_postFDR:
  -in_postFDR
  ${' '.join(["'in_postFDR/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])}
#end if
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out
  'out/output.${gxy2omsext("mztab")}'
#end if
#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_cm
  'out_cm/output.${gxy2omsext("consensusxml")}'
#end if
#if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_feat
  ${' '.join(["'out_feat/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("featurexml")) for _ in $in_postFDR if _])}
#end if
#if $in_contaminants:
  -in_contaminants
  'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)'
#end if
#if $in_trafo:
  -in_trafo
  ${' '.join(["'in_trafo/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _])}
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out/output.${gxy2omsext("mztab")}' '$out'
#end if
#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
#end if
#if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  ${' '.join(["&& mv -n 'in_postFDR/%(id)s.%(gext)s' 'out_feat/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("featurexml")} for _ in $out_feat if _])}
#end if
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in_cm" argument="-in_cm" type="data" format="consensusxml" optional="false" label="ConsensusXML input, generated by FeatureLinke" help=" select consensusxml data sets(s)"/>
    <param name="in_raw" argument="-in_raw" type="data" format="mzml" multiple="true" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
    <param name="in_postFDR" argument="-in_postFDR" type="data" format="featurexml" multiple="true" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
    <param name="in_contaminants" argument="-in_contaminants" type="data" format="fasta" optional="true" label="Proteins considered contaminants" help=" select fasta data sets(s)"/>
    <param name="in_trafo" argument="-in_trafo" type="data" format="trafoxml" multiple="true" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
    <section name="FragmentMassError" title="Fragment Mass Error settings" help="" expanded="false">
      <param name="unit" argument="-FragmentMassError:unit" display="radio" type="select" optional="false" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
        <option value="auto" selected="true">auto</option>
        <option value="ppm">ppm</option>
        <option value="da">da</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" optional="true" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/>
    </section>
    <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false">
      <param name="assume_all_target" argument="-MS2_id_rate:assume_all_target" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits)" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="out_FLAG">out (Output mzTab with QC information)</option>
      <option value="out_cm_FLAG">out_cm (ConsensusXML with QC information (as metavalues))</option>
      <option value="out_feat_FLAG">out_feat (FeatureXMLs with QC information (as metavalues))</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="mztab">
      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
      <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <collection type="list" name="out_feat" label="${tool.name} on ${on_string}: out_feat">
      <discover_datasets directory="out_feat" format="featurexml" pattern="__name__"/>
      <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
    </collection>
    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
      <filter>OPTIONAL_OUTPUTS is None</filter>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_QualityControl"/>
    <expand macro="manutest_QualityControl"/>
  </tests>
  <help><![CDATA[Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_QualityControl.html]]></help>
  <expand macro="references"/>
</tool>